Abstract: Endogenous Reference Gene is a determining factor in detection the transgenic plants and products by using Qualitative Polymerase Chain Reaction (PCR) and Real-Time Quantitative methods. The system research in cassava endogenous reference genes could lay a foundation for detection of genetically modified cassavas and derived products. Several possible endogenous reference genes of cassava including cyclophilin type 2 (DB934316), Glyceraldehyde-3-phosphate dehydrogenase B subunit (GAPDH, TC445), Actin (the edited sequences of TC2158 and TC3381), Alpha-tubulin (TC8072), Polyubiquitin (TC9946), linamarase (TC1540) were selected from DFCI (http://compbio.dfci.harvard.edu/tgi/plant.html) of cassava ESTS, and seven pairs primers (CP2, Actin, GAPDH, PUBQ2, Tublinα1, Tublinα2 and LAM1) were designed, then their internal consistency were assayed in 22 different cassava varieties and their species specific was also detected in other twelve non-cassava euphorbiaceae species and twenty non-euphorbiaceae species. For GAPDH the identical amplification products were obtained with the DNA samples from 22 different cassava varieties, no amplification products were observed in other twelve non-cassava euphorbiaceae species and twenty non- euphorbiaceae species. As for another six pairs primers (CP2, Actin, PUBQ2, Tublinα1, Tublinα2 and LAM1), the non-specificity amplification products were observed in the non-cassava euphorbiaceae species or non- euphorbiaceae species. These results indicated the GAPDH PCR amplification system was species specific and internal consistency and could be used as the endogenous reference genes for the detection of genetically modified cassavas and derived products.